A hybrid approach for the automated finishing of bacterial genomes

Advances in DNA sequencing technology have improved our ability to characterize most genomic diversity. However, accurate resolution of large structural events is challenging because of the short read lengths of second-generation technologies. Third-generation sequencing technologies, which can yield longer multikilobase reads, have the potential to address limitations associated with genome assembly. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at >99.9% accuracy. Complex regions with clinically relevant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 cholera reference strain, we obtained 14 scaffolds of greater than 1 kb for the experimental data and 8 scaffolds of greater than 1 kb for the simulated data, which allowed us to correct several errors in contigs assembled from the short-read data alone. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly.     

Heat or insulation: behavioral titration of mouse preference for warmth or access to a nest

In laboratories, mice are housed at 20–24°C, which is below their lower critical temperature (≈30°C). This increased thermal stress has the potential to alter scientific outcomes. Nesting material should allow for improved behavioral thermoregulation and thus alleviate this thermal stress. Nesting behavior should change with temperature and material, and the choice between nesting or thermotaxis (movement in response to temperature) should also depend on the balance of these factors, such that mice titrate nesting material against temperature. Naïve CD-1, BALB/c, and C57BL/6 mice (36 male and 36 female/strain in groups of 3) were housed in a set of 2 connected cages, each maintained at a different temperature using a water bath. One cage in each set was 20°C (Nesting cage; NC) while the other was one of 6 temperatures (Temperature cage; TC: 20, 23, 26, 29, 32, or 35°C). The NC contained one of 6 nesting provisions (0, 2, 4, 6, 8, or 10g), changed daily. Food intake and nest scores were measured in both cages. As the difference in temperature between paired cages increased, feed consumption in NC increased. Nesting provision altered differences in nest scores between the 2 paired temperatures. Nest scores in NC increased with increasing provision. In addition, temperature pairings altered the difference in nest scores with the smallest difference between locations at 26°C and 29°C. Mice transferred material from NC to TC but the likelihood of transfer decreased with increasing provision. Overall, mice of different strains and sexes prefer temperatures between 26–29°C and the shift from thermotaxis to nest building is seen between 6 and 10 g of material. Our results suggest that under normal laboratory temperatures, mice should be provided with no less than 6 grams of nesting material, but up to 10 grams may be needed to alleviate thermal distress under typical temperatures.     

Reproductive biology of Datura wrightii: the benefits of a herbivorous pollinator

Background and Aims

A deeper understanding of mutualism can be reached by studying systems with measurable costs and benefits. Most studies of this type focus on an unusual class of obligate, species-specific pollination mutualisms. The interaction between Datura wrightii (Solanaceae) and the hawkmoth Manduca sexta offers similar advantages but greater generality. Adult moths both nectar at and deposit eggs on the same plant; larvae are herbivorous. The antagonistic component of this interaction has been well studied. Here the role of M. sexta as a pollinator of D. wrightii, particularly in the context of this moth''s frequent nectaring visits to the bat-pollinated plant Agave palmeri, is documented.

Methods

Hand-pollinations were used to determine breeding system and the reproductive consequences of mixed loads of A. palmeri and D. wrightii pollen. Plants and moths were caged overnight to assess whether nectaring visits led to fruit and seed set. Finally, pollen deposited on field-collected stigmas was identified, with a particular focus on documenting the presence of D. wrightii and A. palmeri grains.

Key Results

Datura wrightii is highly self-compatible, and a visit that deposits either outcross or self pollen almost doubles fruit and seed set compared with unvisited flowers. Manduca sexta transferred enough pollen to produce fruit and seed sets comparable to hand-pollination treatments. Agave palmeri did not interfere with D. wrightii success: in the field, stigmas received almost pure D. wrightii pollen, and hand-addition of large quantities of A. palmeri pollen had no measurable effect on fruit and seed set.

Conclusions

The floral visitation component of the D. wrightii–M. sexta interaction is indeed mutualistic. This finding is essential background to future development of this interaction as a model system for studying mutualism''s costs and benefits. It is already proving valuable for dissecting third-species effects on the outcome of mutualism. Results indicate that M. sexta''s heavy visitation to A. palmeri has no negative effect on the benefits conferred to D. wrightii. However, it can be predicted to augment M. sexta populations to the point where the costs of the interaction begin to exceed its benefits.Key words: Datura wrightii, Agave palmeri, pollination, herbivory, mutualism     

Galectin-3 and galectin-1 bind distinct cell surface glycoprotein receptors to induce T cell death

Galectins are a family of mammalian beta-galactoside-binding proteins that positively and negatively regulate T cell death. Extracellular galectin-1 directly induces death of T cells and thymocytes, while intracellular galectin-3 blocks T cell death. In contrast to the antiapoptotic function of intracellular galectin-3, we demonstrate that extracellular galectin-3 directly induces death of human thymocytes and T cells. However, events in galectin-3- and galectin-1-induced cell death differ in a number of ways. Thymocyte subsets demonstrate different susceptibility to the two galectins: whereas galectin-1 kills double-negative and double-positive human thymocytes with equal efficiency, galectin-3 preferentially kills double-negative thymocytes. Galectin-3 binds to a complement of T cell surface glycoprotein receptors distinct from that recognized by galectin-1. Of these glycoprotein receptors, CD45 and CD71, but not CD29 and CD43, appear to be involved in galectin-3-induced T cell death. In addition, CD7 that is required for galectin-1-induced death is not required for death triggered by galectin-3. Following galectin-3 binding, CD45 remains uniformly distributed on the cell surface, in contrast to the CD45 clustering induced by galectin-1. Thus, extracellular galectin-3 and galectin-1 induce death of T cells through distinct cell surface events. However, as galectin-3 and galectin-1 cell death are neither additive nor synergistic, the two death pathways may converge inside the cell.     

Do Male and Female Cowbirds See Their World Differently? Implications for Sex Differences in the Sensory System of an Avian Brood Parasite

Background

Male and female avian brood parasites are subject to different selection pressures: males compete for mates but do not provide parental care or territories and only females locate hosts to lay eggs. This sex difference may affect brain architecture in some avian brood parasites, but relatively little is known about their sensory systems and behaviors used to obtain sensory information. Our goal was to study the visual resolution and visual information gathering behavior (i.e., scanning) of brown-headed cowbirds.

Methodology/Principal Findings

We measured the density of single cone photoreceptors, associated with chromatic vision, and double cone photoreceptors, associated with motion detection and achromatic vision. We also measured head movement rates, as indicators of visual information gathering behavior, when exposed to an object. We found that females had significantly lower density of single and double cones than males around the fovea and in the periphery of the retina. Additionally, females had significantly higher head-movement rates than males.

Conclusions

Overall, we suggest that female cowbirds have lower chromatic and achromatic visual resolution than males (without sex differences in visual contrast perception). Females might compensate for the lower visual resolution by gazing alternatively with both foveae in quicker succession than males, increasing their head movement rates. However, other physiological factors may have influenced the behavioral differences observed. Our results bring up relevant questions about the sensory basis of sex differences in behavior. One possibility is that female and male cowbirds differentially allocate costly sensory resources, as a recent study found that females actually have greater auditory resolution than males.